The fatal accident happened in the 250cc qualifying as the riders approached the Mathers Cross section of the course – the fastest part of the circuit.
The 125, 250 and 400 practice session last night was cancelled following the fatal accident on the first lap of the session which also involved and Darren Burns.
McGuinness and Rutter (right) swapped positions at the top of the qualifying leaderboard as they battled it out around the 8.9-mile circuit for the coveted pole position slot on the starting grid, with McGuinness on his HM Plant Honda posting the fastest lap of the evening at 123.03mph.
The 35-year-old Morecambe rider was clocked at 198mph through the speed trap on the ultra-fast blast to University Corner, with his top speed matched by Rutter on the official JHP NW200 Ducati.
McGuinness' best time was just over half-a-second better than 11-times winner Rutter, who briefly topped the session last night before McGuinness went back out onto the Triangle circuit with a new set of Dunlop tyres and reclaimed the advantage, which he held until the end of the session.
Guy Martin was in the mix throughout on his Hydrex Bike Animal Honda and secured a front row start with a lap of 121.85mph, two-and-a-half seconds behind McGuinness.
Relentless by TAS Suzuki rider, Cameron Donald, also impressed in Portstewart as he finished ahead of team-mate, Bruce Anstey, in fourth.
AIM Yamaha's Steve Plater could only manage the sixth fastest time of the night as his machine seemed to be losing out on top speed, with statistics indicating the English rider was 8mph down on his main Superbike rivals, McGuinness and Rutter, on the fastest part of the course.
The top Northern Ireland rider was Denver Robb from Ballymena, who was also clocked through the speed trap at 198mph on his Mar-Train Racing Suzuki.
Robb was ninth on the time-sheets with a speed of 119.83mph, while Dungannon's Ryan Farquhar was 12th and Adrian Archibald from Ballymoney 13th on his AMA Suzuki.
Uel Duncan Racing's Gary Johnson was 10th on his Robinson Concrete Honda, finishing one place ahead of Ian Hutchinson on the AIM Yamaha. 'Hutchy' failed to qualify on Tuesday evening after experiencing mechanical trouble but will now start tomorrow's key Superbike races from the fourth row of the grid after achieving a best speed of 119.48mph.
William Dunlop was 16th on his Lilley Electrical Suzuki, while Scotsman Ian Simpson, who is riding at the event for Iain Duffus and Brian Morrison's DMR Team, was 21st.
Plater leads the way in the Supersport class on his AIM Yamaha at 117.90mph, from Carrickfergus man Alastair Seeley and Keith Amor.
Ian Hutchinson (AIM Yamaha), John McGuinness (Padgetts Honda) and Bruce Anstey (TAS Suzuki) completed the top six.
Wilson Craig Racing's Amor will start from pole in the Superstock race, with a lap of 121.14mph putting him at the head of affairs in the competitive production-based class.
Seeley was second from Michael Rutter, Bruce Anstey, Conor Cummins and Cameron Donald.
John McGuinness will start the 250 race from pole position after he established the fastest time on Tuesday evening, with Michael Dunlop second and Paul Robinson third.
Michael Wilcox was the fastest 125 rider on Tuesday, while Leo Aldersley was the top 400cc competitor.
RESULTS:
SUPERBIKE: 1 John McGuinness 123.03mph; 2 Michael Rutter 122.72mph; 3 Guy Martin 121.85mph; 4 Cameron Donald 121.81mph; 5 Bruce Anstey 121.75mph; 6 Steve Plater 120.87mph; 7 Ian Lougher 120.20mph; 8 Keith Amor 119.95mph; 9 Denver Robb 119.83mph; 10 Gary Johnson 119.72mph.
SUPERSPORT: 1 Steve Plater 117.90mph; 2 Alastair Seeley 117.69mph; 3 Keith Amor 117.18mph; 4 Ian Hutchinson 116.70mph; 5 John McGuinness 116.65mph; 6 Bruce Anstey 116.45mph.
SUPERSTOCK: 1 Keith Amor 121.142mph; 2 Alastair Seeley 120.42mph; 3 Michael Rutter 120.37mph; 4 Bruce Anstey 119.57mph; 5 Conor Cummins 119.29mph; 6 Cameron Donald 118.85mph.